Link to this post | posted 04 Jun, 2018 00:07
dbolliva	Which DSB repair gene does it hit on? It seems like there are a number of proteins that are involved in dsb repair.

Link to this post | posted 04 May, 2018 03:03
dbolliva	Welkin may weigh in on this later, but the question I would ask is whether this is truly a function. There are a few examples of proteins given a function that really isn't one, but my understanding is that we are really trying to limit function calls to proteins that have a function.

Link to this post | posted 24 Mar, 2018 18:19

dbolliva

In answer to your first question, the function field is indeed the field/box in DNA Master. Placing the function in this box is to make creation of the minimal file possible and straightforward. In essence the function is listed in two places, following the F in the notes box and in the function box. If you put functions directly into the product field, it will mess up the process of automatically adding Hypothetical Protein for all of the genes with no function as you create the minimal file. Your screenshot of the minimal file also looks right to me. It seems empty after the complete notes, but it makes the submission process easier. The new online version of the manual seems to have submitters do more than the older paper version of the bioinformatics manual. Edited 24 Mar, 2018 18:26

Link to this post | posted 21 Mar, 2018 16:19
dbolliva	It is not on the official list so I would not call it. Though there were some hits to PLA2, I think the evalues ended up not being good enough. Ultimately I think the people at Pitt will clean this up and make them all NKF.

Link to this post | posted 08 Feb, 2018 01:52
dbolliva	Veronique, You probably already know this, but my go to for slippery sequences is the Xu, Hendrix, and Duda paper: https://doi.org/10.1016/j.molcel.2004.09.006 That sequence you list is not represented in any of their tables but still could be one……. I agree with you that those other sequences do not look slippery at all to me. Just my two cents… and it might not be worth that. Dave

Link to this post | posted 08 Feb, 2018 01:40

dbolliva

Jeremy, I don't have the answer to the question you are asking but I do have a comment about the M smeg infection. We have been using very dense cultures that I suspect are not at all in log phase but are probably reaching stationary phase. I also have done this with a completely different bacterium and also get good results from stationary phase infections. I would recommend getting it really dense and trying the infection then. Dave

Link to this post | posted 17 Jan, 2018 17:52
dbolliva	Claire, I can tell from looking that things have been added since October to this list. For example we just added two functions that are found in the genome of Tesla and they are at the bottom of the list. Best, Dave

Link to this post | posted 17 Jan, 2018 15:37
dbolliva	Joe, One way to tell is to look at the phage page on phagesdb. It has a heading for whether it has been phamerated. I peeked at Bromden and it currently is not listed as being phamerated yet. Best, Dave

Link to this post | posted 15 Jan, 2018 04:20

dbolliva

Beckie, I think the big question to ask is what does it mean to be an FIC protein. When I did a quick search I found that these proteins contain a domain that is HPFXXGNG and indeed your protein has this conserved domain. What I also found was that this family of proteins has a member called DOC that stands for death on curing and somehow leads to cell death if the P1 prophage is lost. In this case the lysogen is carried as a plasmid and can be lost during cell division but if cells lose the plasmid lysogen they die. This seems like a really cool and possible function for your protein. Hopefully Welkin will look at this and make a decision. Best, Dave

Link to this post | posted 30 Dec, 2017 17:43
dbolliva	Welkin, I thinke the carboxylate amine ligase is a better choice for the reason you mentioned. Best, Dave